Prognostication and clinical management of prostate cancer (PCA) is one the most complex and controversial issues in contemporary oncology. Our overarching goal is to develop tissue based molecular tests to distinguish indolent from aggressive PCA prior to treatment. Our proposal will address several critical issues related to the development of a clinically relevant molecular signature of PCA: (1) We use PCA specific death as the clinical endpoint; (2) We will employ 3 well defined patient populations from Sweden with long term and complete clinical follow up; (3) We use tumor enriching methods such as laser capture microdissection (LCM) due to the cellular heterogeneity of PCA. These guiding principles have been organized into 3 Specific Aims: In Aim 1, we use 10OK single nucleotide polymorphism (SNP) arrays for the detection of Loss of Heterozygosity (LOH), homozygous deletions and gene amplification events to generate genome-wide genetic maps at a resolution of 9Kb. Combining this molecular signature data with clinical data on PCA biopsy samples from 96 consecutive frozen samples from men diagnosed in Orebro, Sweden with clinically localized PCA of whom 40 died of PCA and 30 of other causes, we will develop a molecular signature to distinguish aggressive from indolent PCA. In Aim 2, we test and validate this molecular profile using a bead-based nanotechnology to assess for somatic alterations in the DNA that can be applied on formalin-fixed paraffin embedded samples from the nationwide cohort of prostatectomies in Sweden (n=600) and two Watchful Waiting cohorts (n=620) with a projected 200 and 120 PCA specific deaths, respectively. In Aim 3, we will employ tissue microarrays from the Swedish Prostatectomy and the Watchful Waiting cohorts and evaluate combinations of biomarkers by quantitative analysis of immunohistochemistry, immunofluorescence (AQUA), in situ hybridization (ISH)or fluorescence in situ hybridization(FISH). We expect to develop in situ tests that will be transportable to other laboratories for clinical validation. At the conclusion of this proposal, we expect to have refined and fully validated molecular predictors of PCA death as well as indolent PCA that is appropriate for further clinical development.